PE-Assembler specifications


Unique identifier OMICS_00025
Name PE-Assembler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes




No version available


Publication for PE-Assembler

PE-Assembler citations


Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

BMC Genomics
PMCID: 3469383
PMID: 22884033
DOI: 10.1186/1471-2164-13-385
call_split See protocol

[…] Low quality reads produced by the Illumina GAIIx method were filtered using the ShortRead 1.8.0 package []. Assembly for each strain was performed with the PE-Assembler 1.1 []. IMAGE 2.1 [] was used to close gaps as it locally assembles reads aligning to contig ends. Bowtie 0.12.5 short read aligner [] was used to align reads to the resulting contigs and […]


Genomic acquisition of a capsular polysaccharide virulence cluster by non pathogenic Burkholderia isolates

Genome Biol
PMCID: 2945791
PMID: 20799932
DOI: 10.1186/gb-2010-11-8-r89

[…] em repeats were excluded. Functional classification of SNPs was performed using gene co-ordinates from the BtE264 reference genome. De novo assembly of the BtE555 paired-end reads was performed using PE-Assembler, an in-house toolkit (PA and WS, manuscript in preparation). De novo assembled contigs were mapped to the reference Bt E264 genome using Nucmer [] and Contig Aligner []. Genes on contigs […]

PE-Assembler institution(s)
Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore; School of Computing, National University of Singapore, Singapore
PE-Assembler funding source(s)
Supported by MOE AcRF Tier 2 funding R-252-000-444-112 and Agency for Science, Technology and Research (A*STAR).

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